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Phenotypic profiling of the human genome by time-lapse microscopy reveals cell division genes

Nature volume 464, pages 721–727 (2010)Cite this article

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Abstract

Despite our rapidly growing knowledge about the human genome, we do not know all of the genes required for some of the most basic functions of life. To start to fill this gap we developed a high-throughput phenotypic screening platform combining potent gene silencing by RNA interference, time-lapse microscopy and computational image processing. We carried out a genome-wide phenotypic profiling of each of the ∼21,000 human protein-coding genes by two-day live imaging of fluorescently labelled chromosomes. Phenotypes were scored quantitatively by computational image processing, which allowed us to identify hundreds of human genes involved in diverse biological functions including cell division, migration and survival. As part of the Mitocheck consortium, this study provides an in-depth analysis of cell division phenotypes and makes the entire high-content data set available as a resource to the community.

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Figure 1: Data analysis and hit detection.
Figure 2: Rescue experiments.
Figure 3: Gene Ontology (GO) terms distribution and event order maps.
Figure 4: Time-resolved heat map.
Figure 5: Functional analysis of spindle phenotypes.

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Acknowledgements

We thank J. Gagneur for suggestions on data processing; S. Berthoumieux for assistance in computation; Y. Sun for coordination support in Mitocheck; U. Ringeisen for help in preparing the figures; S. Winkler and L. Burger and EMBL’s electronic and mechanical workshops for support in microscope development; Olympus Soft Imaging Solutions (OSIS) and Olympus Europe for collaboration; Leica Microsystems for collaboration; Applied Biosystems for providing unpublished validation data of the siRNA library; and all our colleagues in the Mitocheck consortium for collaboration. This project was funded by grants to J.E. (within the Mitocheck consortium by the European Commission (LSHG-CT-2004-503464) as well as by the Federal Ministry of Education and Research (BMBF) in the framework of the National Genome Research Network (NGFN) (NGFN-2 SMP-RNAi, FKZ01GR0403)), to R.P. (BMBF NGFN2 SMP-Cell, FKZ01GR0423) as well as to J.E. and R.P. by the Landesstiftung Baden Wuerttemberg in the framework of the research programme ‘RNS/RNAi’. R.D. is supported by the Wellcome Trust.

Author Contributions B.N. developed the primary screen assay. P.R., H.E., B.N. and J.B. generated the data for the primary and validation screen. T.W. and M.H. developed the image processing software. T.W., J.-K.H., G.P., and W.H. analysed the data. J.-K.H., V.S. and R.S. performed the bioinformatics analysis. B.N., P.R., J.B., T.W. and C.Co. conducted the quality control and manual annotation. U.L., C.Co., F.S. and R.P. developed the HT microscope platform. H.E. and R.P. developed the HT transfection platform. J.-K.H. and R.D. created the Mitocheck database and website. C.Ce. and R.P. designed the manual annotation database. J.B., C.Co., B.N. and A.W. created the data for the spindle assay. R.K. and R.E. provided IT support. I.P. and A.A.H. provided the BAC cell pools. M.H.A.S., C.Ch. and D.W.G. provided reagents. J.-M.P. coordinated the Mitocheck consortium. J.E. coordinated and supervised the project and wrote the manuscript.

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Author notes

  1. Jean-Karim Hériché, Holger Erfle, Phill Rogers, Michael Held & Urban Liebel

    Present address: Present addresses: MitoCheck Project Group, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, D-69117 Heidelberg, Germany (J.-K.H.); BIOQUANT Centre University Heidelberg, INF 267, D-69120 Heidelberg, Germany (H.E.); 3-V Biosciences GmbH, Wagistrasse 27, 8952 Schlieren, Switzerland (P.R.); Institute of Biochemistry, Swiss Federal Institute of Technology Zurich (ETHZ), Schafmattstrasse 18, CH-8093 Zurich, Switzerland (M.H.); Karlsruhe Institute of Technology KIT, Herrmann-von-Helmholtz Platz 1, D-76344 Eggenstein-Leopoldshafen, Germany (U.L.).,

  2. Beate Neumann and Thomas Walter: These authors contributed equally to this work.

Authors and Affiliations

  1. MitoCheck Project Group,,

    Beate Neumann, Thomas Walter, Jutta Bulkescher, Holger Erfle, Christian Conrad, Phill Rogers, Michael Held & Urban Liebel

  2. Gene Expression and,,

    Annelie Wünsche & Jan Ellenberg

  3. Cell Biology/Biophysics Units, Structural and,,

    Holger Erfle, Christian Conrad, Cihan Cetin, Catherine Chapuis & Rainer Pepperkok

  4. Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, D-69117 Heidelberg, Germany ,

    Venkata Satagopam & Reinhard Schneider

  5. Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1HH, UK ,

    Jean-Karim Hériché & Richard Durbin

  6. Max Planck Institute for Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, D-01307 Dresden, Germany ,

    Ina Poser & Anthony A. Hyman

  7. Institute of Biochemistry, Swiss Federal Institute of Technology Zurich (ETHZ), Schafmattstrasse 18, CH-8093 Zurich, Switzerland ,

    Michael H. A. Schmitz & Daniel W. Gerlich

  8. Leica Microsystems CMS GmbH, Am Friedensplatz 3, D-68165 Mannheim, Germany ,

    Frank Sieckmann

  9. European Bioinformatics Institute, European Molecular Biology Laboratory, Cambridge CB10 1SD, UK

    Gregoire Pau & Wolfgang Huber

  10. Division of Theoretical Bioinformatics, German Cancer Research Center, Im Neuenheimer Feld 267, D-69120 Heidelberg, Germany,

    Rolf Kabbe & Roland Eils

  11. Institute for Molecular Pathology, Dr Bohr Gasse 7, A-1030 Vienna, Austria ,

    Jan-Michael Peters

Authors
  1. Beate Neumann
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Corresponding author

Correspondence to Jan Ellenberg.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Information

This file contains Supplementary Methods, Supplementary References, Supplementary Figures 1-11 with legends and Legends for Supplementary Movies 1-14. (PDF 2252 kb)

Supplementary Tables

This zipped file contains Supplementary Tables 1-7. (ZIP 580 kb)

Supplementary Movies 1

This zipped file contains Supplementary Movies 1-15 which show an overview of the representative morphology for each of the sixteen classes shown in Figure 1b. (ZIP 32444 kb)

Supplementary Movies 2

This zipped file contains Supplementary Movies 16-30 which show the highlighted single cell from movie 1-15 (Figure 1b). (ZIP 1991 kb)

Supplementary Movies 3

This zipped file contains Supplementary Movies 31-40 which show the spindle morphology phenotypes represented in Figure 5. (ZIP 26408 kb)

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Neumann, B., Walter, T., Hériché, JK. et al. Phenotypic profiling of the human genome by time-lapse microscopy reveals cell division genes. Nature 464, 721–727 (2010). https://doi.org/10.1038/nature08869

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